Organic Acids Testing

The Clinical Significance of Organic Acids Testing to Mental Health – How Fungal, Bacterial, Mitochondrial, and Other Test Markers Influence the Brain

Kurt Woeller, D.O.

Organic acids testing is diagnostic tool that every healthcare practitioner should know about.  Whether you are a family practitioner, psychiatrist, a nutritionist, or other type of practitioner, the information provided by organic acids testing can help identify underlying causes of a variety of chronic illnesses, including the symptoms of autism, neuropsychiatric disorders like depression and anxiety, and neurodegenerative disorders like Alzheimer’s disease.  Below is a review of some of the most clinically significant markers measured with organic acids testing to mental health and the health of the brain in general. 

Many of the case studies reviewed in presentations about organic acids testing involve patients with autism.  While autism may not typically be considered a mental health disorder, it is a neurodevelopmental disorder and many autistic individuals suffer with mental symptoms such as anxiety and depression, along with associated behavioral problems.  Many patients with autism also have mitochondrial dysfunction and chronic infections (like Candida and clostridia), which are measured with organic acids testing. (1)

Mitochondria are linked to every organ system in the body, including the brain, and there markers for mitochondrial function in organic acids testing. Without adequate mitochondrial function, neurons cannot function appropriately to produce neurochemicals such as dopamine and serotonin.  Mitochondria are damaged by various endogenous toxins produced by Candida (a fungus) such as tartaric acid and citramalic acid. Also, certain clostridia bacteria produce propionic acid which damages mitochondria. Candida and clostridia are both measured with organic acids testing.  Mitochondria are also damaged by oxalate, which is produced by Candida and some molds, and is also measured with organic acids testing. Certain molds like Aspergillus produce mycotoxins which directly damage mitochondria. Organic acids testing specifically measures candida toxins, bacteria toxins, and mold toxins, along with mitochondria markers. (2, 3)

Clostridia bacteria can produce various compounds like HPHPA, 4-Hydroxyphenylacetic acid and 4-Cresol (all measured with organic acids testing), and are known to inhibit dopamine metabolism. These chemicals inhibit Dopamine-Beta Hydroxylase which causes neuronal dopamine levels to rise. This has been associated with paranoia and schizophrenia. Also, the breakdown products of dopamine are neurotoxic and cause brain receptor damage.  Chronic infections and the compounds produced from them such as bacteria lipopolysaccharides (LPS), along with elevated cortisol (seen in hypothalamic-pituitary-adrenal dysfunction), viral infections, and beta-amyloid and niacin deficiency (seen in schizophrenia) can trigger tryptophan metabolism problems. Tryptophan is the amino acid precursor to serotonin. In the presence of these chronic stressors, tryptophan conversion to serotonin is reduced. This can lead to depression and anxiety. Elevated tryptophan metabolites can lead to increased quinolinic acid (QA).  (4)

Quinolinic acid is neurotoxic and measured with organic acids testing. It is an NDMA receptor agonist, which is linked to various mental health disorders (anxiety, depression, suicidal ideation) and chronic neurodegenerative diseases (Alzheimer’s, Huntington’s). Quinolinic acid can also block acetylcholine production (linked to memory) and gamma-amino-butyric acid (which can trigger anxiety and panic). (5)

The aforementioned markers in organic acids testing are some of the most clinically significant to mental health and brain function, though there are many other examples.  This information is critical for mental health professionals to help deepen their knowledge about sophisticated testing and advanced solutions for patient intervention. 


  1. Shaw, W., et. al. Increased Urinary Excretion of Analogs of Krebs Cycle Metabolites and Arabinose in Two Brothers with Autistic Features. Clin Chem 41:1094-1104, 1995.
  2. Shaw, W., et. al. Assessment of antifungal drug therapy in autism by measurement of suspected microbial metabolites in urine with GC/MS. Clinical Practice of Alternative Medicine: 15-26.
  3. Persico AM, et. al. Urinary p-cresol in autism spectrum disorders, Neurotoxicol Teratol. 2013 Mar-Apr;36:82-90, 2012 Sep 10.
  4. Heyes MP, et. al. A mechanism of quinolinic acid formation by brain in inflammatory neurological disease. Attenuation of synthesis from L-tryptophan by 6-chlorotryptophan and 4-chloro-3-hydroxyanthranilate. Brain. 1993 Dec;116 (pt 6):1425-50.
  5. Ganiyu Oboh, et. al. Anticholinesterase and Antioxidative Properties of Aqueous Extract of Cola acuminata Seed In Vitro. Int J Alzheimers Dis. 2014; 2014: 498629.

A New Generation of Organic Acid Testing: Pushing the Limits of Detection with New Technology

Shaw, William Ph.D

More than 50 phenotypically different organic acidemias have been discovered since the first known disease of this type, isovaleric academia, was described in 1966. An organic acid is any compound that generates protons at the prevailing pH of human blood. Although some organic acidemias result in lowered blood pH, other organic acidemias are associated with relatively weak organic acids that do not typically cause acidosis.

Organic acidemias are disorders of intermediary metabolism that lead to the accumulation of toxic compounds that derange multiple intracellular biochemical pathways, including glucose catabolism (glycolysis), glucose synthesis (gluconeogenesis), amino acid and ammonia metabolism, purine and pyrimidine metabolism, and fat metabolism. The accumulation of an organic acid in cells and fluids (plasma, cerebrospinal fluid, or urine) leads to a disease called organic academia, or organic aciduria.

Although this technology has commonly been used for diagnosing genetic disease in children, genetic diseases in adults have also been detected with it. New applications of organic acid testing include detection of factors in psychiatric disorders, mitochondrial disease and dysfunction, and exposure to a wide variety of toxic chemicals from the environment, and assessment of inflammation due to overproduction of quinolinic acid from tryptophan.

Testing now includes markers for the following metabolites:

  • Glycolysis
  • Krebs Cycle
  • Amino acid Metabolism
  • DNA, RNA metabolism
  • Neurotransmitter metabolism
  • Organophosphate metabolism
  • Yeast, fungal markers
  • Markers for beneficial bacteria
  • Oxalate markers for kidney stones, genetic disease
  • Specific marker for ammonia toxicity
  • Markers of fatty acid catabolism
  • Metabolic diseases causing autism spectrum disorders
  • Phthalates
  • Solvents
  • Pyrethrins
  • Dry cleaning solvents
  • Preservatives
  • Vinyl chloride
  • Specific Clostridia marker
  • Specific mitochondrial disease markers
  • Vitamin deficiency markers
  • Phosphate marker of bone function
  • Marker for glutathione precursor
  • Genetic screening with extremely sensitive markers

Organic acids are most commonly analyzed in urine because they are not extensively reabsorbed in the kidney tubules after glomerular filtration. Thus, organic acids in urine are often present at 100 times their concentration in the blood serum and thus are detected in urine with greater accuracy and precision than with blood samples. The number of organic acids found in urine is enormous: over 1000 have been detected since this kind of testing started 25 years ago. The challenge of dealing with so many compounds led to the use of gas chromatography-mass spectrometry (GC/MS) to analyze these complex body fluids.

With GC/MS, organic acids are chromatographically separated on the basis of their polarity and volatility and then bombarded by an electron beam that fragments the eluting molecules in a characteristic pattern. The patterns, or spectra, are stored by a computer system and then compared with known spectra that are compiled in a spectral "library." The software then compares an unknown spectrum to all the spectra on the hard drive and prints out those with the best fit. Since a single organic acid analysis generates over 1000 spectra, and each spectrum may consist of 600 ions, the software must be optimized to analyze the data in the most efficient and clinically relevant manner. Recently, the Great Plains Laboratory Inc. increased the sensitivity of this technology by approximately 1000-fold with the use of new triple-quadrupole MS technology so that a large number of toxic compounds can be measured at levels of micromoles/mole creatinine compared with urine compounds, such as vanillylmandelic (VMA), which is measured at levels of millimoles/mole creatinine.

The scope of organic acid testing has been markedly widened by commercial laboratories such that it can monitor physiological changes in nongenetic diseases and offer tremendous help in diagnosis and treatment of most chronic illnesses. Some examples are given below:

An adult with a movement disorder and bilateral temporal arachnoid cysts by brain imaging was found to have very elevated glutaric acid, indicating the presence of the genetic disease glutaric aciduria type 1.1Symptoms of this potentially fatal disorder include headaches, ataxia, memory loss, and many other neurological effects. Treatment with high doses of carnitine may be helpful in relieving symptoms in such cases, and of course such information is important for genetic counseling.

High levels of urine oxalates in an adult with frequent kidney stones led to a closer examination of the patient's dietary history. The patient ate a large spinach salad with pecans almost every day. Spinach is one of the foods highest in oxalates, and all nuts are high in oxalates as well. Treatment is directed at reducing dietary oxalates as well as calcium citrate and vitamin B6 supplementation.

After organic acid testing, a child with autism was found to have very high values (more than four times the upper limit of age-appropiate normals) of the catecholamine metabolites VMA and HVA, indicating a possible neuroblastoma. Follow-up imaging near the spine confirmed the presence of a previously undiagnosed neuroblastoma, likely saving the child's life.

Another child thought to have autism had very low amino acids, and the neurologist recommended high doses of amino acid supplements, which made the child severely ill. Organic acid testing revealed a massive excretion of methylmalonic acid, indicating that the child had methlmalonic aciduria, a severe genetic disorder. Treatment of this disorder requires extensive supplementation with vitamin B12 and a low-protein diet. Continued amino acid supplementation or a high-protein diet might have been fatal.

A person with severe depression was found to have low amounts of the serotonin metabolite 5-hydroxy-indoleacetic acid, which is derived from tryptophan. Depression is associated with decreased brain serotonin. However, the tryptophan metabolite by an alternate pathway, quinolinic acid, was much higher. Quinolinic acid is associated with inflammation such as arthritis and is considered to be neurotoxic, with a probable role in Parkinson's syndrome, Alzheimer's disease, Huntington's disease, and schizophrenia.2,3 The condition eosinophilia myalgia syndrome (EMS), associated with excessive tryptphan intake, is probably not due to tryptophan itself but to the inflammatory effects of its major metabolite quinolinic acid. Quinolinc acid administered by itself generated all of the symptoms of EMS.4,5 This research indicates that various conspiracy theories about contaminated tryptophan batches as the cause of EMS are unnecessary and probably wrong. 100% pure tryptophan at high enough doses will produce significant quantities of toxic quinolinic acid and EMS in susceptible individuals. Administration of 5-hydroxytryptophan (5-HT or 5-HTP) is a much safer option than tryptophan since 5-HT cannot be converted to the neurotoxic quinolinic acid, whereas only about 1% of tryptophan is converted to serotonin.6 Both the serotonin metabolite and quinolinic acid are measured by organic acid testing (Figure 1).

I recently proved that the dibiosis marker 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (HPHPA), the predominant dihydroxy-phenylpropionic acid isomer in urine measured in the organic acid test, is due to a combination of human metabolism and the metabolism by a group of Clostridia species, including but not limited to C. difficile.7 The same article indicates that 3,4-dihydroxyphenylpropionic acid (DHPPA) is a marker for beneficial bacteria in the gastrointestinal tract such as Lactobacilli, Bifidobacteria, and E. coli. The exception is one species of Clostridia orbiscindens that can convert the flavonoids luteolin and eriodictyol (which occur only in a relatively small food group that includes parsley, thyme, celery, and sweet red pepper) to DHPPA. The quantity of C. orbiscindens in the gastrointestinal tract is negligible (approximately 0.1% of the total bacteria) compared with the predominant flora of Lactobacilli, Bifidobacteria, and E. coli.7 DHPPA is an antioxidant that lowers cholesterol, reduces proinflammatory cytokines, and protects against pathogenic bacteria.

Outdated literature has referred to HPHPA as due to dietary origin based mainly on conjecture, but this conjecture was clearly disproved by my 2010 article which indicates that the metabolite is abolished by the antibiotic metronidazole.8 DHPPA, a different isomer, has been claimed to be a metabolite of Pseudomonas species, but the literature indicates that this compound is formed by the in vitro action of these species on quinolone, a component of coal tar – a substance missing from the diet of virtually all humans.9

HPHPA has been one of the most useful clinical markers in recent medical history. Treatment of individuals with high urinary values with metronidazole, vancomycin, or high doses of probiotics has led to significant clinical improvements or remissions of psychosis, tic disorders, seizures, autistic behaviors, hyperactivity, chronic fatigue syndrome, and obsessive compulsive behavior.

One of the newest aspects of organic acid testing is the screening for 74 different toxic chemicals in the environment by testing their organic acid metabolites. Solvents such as benzene, toluene, styrene, and others may be present for only short periods in body fluids and may also be lost in transit due to their volatility, but their metabolites are very stable. Using this screening technique, most metabolites of different organophosphates and pyrethrins can be measured as well as trichloroethylene, tetrachloroethylene, and vinyl chloride. Phthalates, an extremely toxic group of compounds implicated in infertility and abnormal sexual development in both males and females, can be measured by their metabolite phthalate, a specific chemical entity.

The chemical structure of phthalic acid (or phthalates) is nearly identical to quinolinic acid. A toxic effect occurs when phthalic acid competitively inhibits the reaction by which quinolinic acid is converted to the beneficial coenzyme NAD. High concentrations of phthalic acid or quinolinic acid may be associated with increased toxicity due to phthalate blockage of NAD formation and potential mitochondrial dysfunction due to deficient NAD for mitochondrial energy production.

One of the most important advances in the organic acid test is the addition of a biochemical marker, tiglylglycine, as a specific indicator for mitochondrial dysfunction.11 Mitochondrial dysfunction has been implicated in Parkinson's and Alzheimer's syndromes, diabetes, autism, chronic fatigue syndrome, aging, and many others. Tiglylglycine has been shown to be elevated in the urine in mitochondrial disorders involving defects of complexes I, II, III, and IV, protein complexes attached to the mitochondrial membrane that are involved in energy production. In addition to mutations in mitochondrial or nuclear DNA, mitochondrial dysfunction may also be due to exposures to toxic chemicals such as organophosphates and the solvent trichloroethylene. The advantage of the organic acid test is that if a mitochondrial dysfunction is detected, a number of different toxic chemicals implicated in mitochondrial damage can be reviewed to find the potential cause. Trichloroethylene has been found as a contaminant in the municipal water supply of many cities in both the US and Canada, and is used as a degreaser military bases and as a common solvent throughout the chemical industry. Mitochondrial disorders can be treated with a cocktail of nutritional substances including coenzyme Q10, carnitine, riboflavin, and others, when chemical exposure is not detected. If toxic chemicals are found, treatment with the Hubbard protocol can be highly successful for the removal of a wide array of toxic substances.12

Clinical References:

  • 1. Martinez-Lage J et al. Macrocephaly, dystonia, and bilateral temporal arachnoid cysts: glutaric aciduria type 1. Childs Nerv Sys. 1994;10(3): 198-203.
  • 2. Guillemin GJ et al. Quinolinic acid in the pathogenesis of Alzheimer's disease. Adv Exp Med Biol. 2003;527:167-176.
  • 3. Stoy N et al. Tryptophan metabolism and oxidative stress in patients with Huntington's disease. J Neurochem. 20015;93:611-623.
  • 4. Silver RM et al. Scleroderma, fasciitis, and eosinophilia associated with the ingestion of tryptophan. N Engl J Med. 1990;322(13):874-881.
  • 5. Noakes R, Spelman L, Williamson R. Is the L-tryptophan metabolite quinolinic acid responsible for eosinophilic fasciitis? Clin Exp Med. 2006;6(2):60-64.
  • 6. Shah GM et al. Biochemical assessment of niacin efficiency among carcinoid cancer patients. Am J Gastroenterol. 2005;100:2307-2314.
  • 7. Shaw W. Increased urinary excretion of a 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (HPHPA), an abnormal phenylalanine metabolite of Clostridia species in the gastrointestinal tract, in urine samples from patients with autism and schizophrenia. Nutr Neurosci. 2010;13(3):1-10.
  • 8. Kumps A, Duez P, Mardens Y. Metabolic, nutritional, latrogenic, and artifactual sources of urinary organic acids: a comprehensive table. Clin Chem. 2002,48:708-717.
  • 9. Shukla OP. Microbial transformation of quinolone by a pseudomonas sp. Appl Environ Microbiol. 1986;51(6):1332-1342.
  • 10. Fukuwatari T et al. Phthalate esters enhance quinolinate production by inhibiting alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarbocylase (ACMSD), a key enzyme of the tryptophan pathway. Toxicol Sci. 2004;81:302-308.
  • 11. Bennett M et al. Tiglylglycine excreted in urine in disorders of isoleucine metabolism and the respiratory chain measured by stable isotope dilution GC-MS. Clin Chem. 1994;40(10):1879-1833.
  • 12. Shaw W. The unique vulnerability of the human brain to toxic chemical exposure and the importance of toxic chemical evaluation and treatment in orthomolecular psychiatry. J Orthomol Med. 2010;25(3).